limix bgen-reader-py issues

limix / bgen-reader-py

A BGEN file format reader.

MIT License

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issues

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Conda: Python versions >3.9

#50 chrisief opened 6 months ago
0
Fix sample files by moving them to a new GitHub repro.

#49 CarlKCarlK opened 10 months ago
0
example_filepath reports AWS error

#48 CarlKCarlK opened 10 months ago
3
Error while creating metafile bgen.metadata

#47 cnl27 opened 10 months ago
2
Minor bug in docs

#46 CarlKCarlK opened 1 year ago
0
bgen-reader no longer working on windows

#45 CarlKCarlK opened 2 years ago
0
Allow bgen-reader to work with files in read-only directories

#44 CarlKCarlK opened 2 years ago
0
GitHub Action python-package.yml seems to have rotted

#43 CarlKCarlK opened 2 years ago
1
Can't open bgen using symbolic links

#42 jordanero opened 2 years ago
7
fix issue 40

#41 CarlKCarlK closed 3 years ago
0
bgen_reader.allele_expectation allocates memory based on unindexed genotype

#40 jordanero opened 3 years ago
3
ImportError

#39 cybluetree closed 3 years ago
2
Saving metadata in different dir as bgen file

#38 evigorito closed 3 years ago
8
index out of range in bgen["variants"]

#37 ScarlettWang532 closed 3 years ago
3
Empty bgen file might cause division by zero.

#36 horta opened 3 years ago
0
Could not open genotype

#35 fbeghini closed 3 years ago
17
Update bgen2 to use cbgen

#34 CarlKCarlK closed 3 years ago
1
More options for control of behavior in read_genotype

#33 eric-czech closed 3 years ago
16
Export infer_metafile_filepath properly

#32 horta opened 4 years ago
0
Make use of pooch for example files

#31 horta opened 4 years ago
0
Feature request: bulk distributed access

#30 tomwhite opened 4 years ago
35
Library fails on *.bgen files larger than 2Gbtyes (2**31)

#29 CarlKCarlK closed 4 years ago
2
Can't figure out dev build on Derbin

#28 CarlKCarlK closed 4 years ago
2
ci\before-build-win.bat references bgen install.bat that no longer exists

#27 CarlKCarlK closed 4 years ago
2
Just Python 3?

#26 CarlKCarlK closed 4 years ago
1
read_bgen ignores new file contents

#25 CarlKCarlK closed 4 years ago
1
variant position is returning negative numbers

#24 CarlKCarlK closed 4 years ago
3
Variant info performance seems slow as # of variants goes to 1M+

#23 CarlKCarlK closed 4 years ago
8
Can't retrieve large.bgen test file

#22 CarlKCarlK closed 4 years ago
5
pickle error on dask cluster

#21 jeremymcrae closed 4 years ago
1
Segmentation fault (core dumped)

#20 alexanderbuchholz closed 4 years ago
12
GEN-reader?

#19 hoangthienan95 closed 4 years ago
6
Suppress "setupterm() failed: TERM=xterm-256color not found in database or too generic" warning

#18 horta closed 5 years ago
0
RuntimeError: Could not open /path/to/test.bgen.metadata

#17 torstees closed 5 years ago
3
Genotypes in probabilities?

#16 Hoeze opened 5 years ago
8
index out of range

#15 nurfatimaj closed 5 years ago
13
Lots of issues with python 2.7

#14 torstees closed 5 years ago
1
sporadic error when reading in genotypes

#13 arminschoech closed 5 years ago
3
Add sample_file option to read_bgen

#12 HannahVMeyer closed 6 years ago
0
Error when installing with pip

#11 dissectroslin closed 6 years ago
4
Add example for using batches if you want to accessing all the genome

#10 hyanwong closed 6 years ago
11
'bgen_reader._ffi' not found

#9 seafloor closed 6 years ago
2
Add support for phased data (and return extra variant information)

#8 hyanwong closed 6 years ago
42
I get "Error while storing buffer: Permission denied"

#7 hyanwong closed 6 years ago
5
Reading variants takes longer than a minute, possible to only read subset of variants?

#6 ParsaAkbari closed 6 years ago
3
Version 1.0.1 won't run unless you manually install everything

#5 torstees closed 6 years ago
3
Retrieving all genotypes for a single sample is very slow

#4 arinbjornk closed 6 years ago
2
Deal with NULL ids

#3 Bonder-MJ closed 6 years ago
0
Print out whether there are sample ids

#2 horta closed 6 years ago
0
Print out the bgen file specification version

#1 horta closed 6 years ago
0